1. Introduction
DNA damage occurs frequently throughout all aspects of life from a variety of sources. Exogenous DNA damaging sources include physical or chemical agents, such as ionizing radiation, UV light, environmental mutagens, or chemotherapeutic treatments. These exogenous agents induce DNA strand breaks, helix-distorting photolesions, and intra- or inter-strand crosslinks (Chatterjee & Walker, 2017). There are also many damaging agents residing in cells. The most common one is reactive oxygen species (ROS), which is generated during cell metabolism and can induce high amount of oxidative damage in DNA (Cooke et al., 2003). Additionally, cytosine deamination (loss of an amino group), depurination (loss of a base), and nucleotide misincorporation during replication or recombination also occur at high frequency to form endogenous DNA damage (Ciccia & Elledge, 2010). These lesions may cause a variety of structural alterations within the DNA, thereby representing a major threat to the integrity of the genome.
DNA damage can trigger a wide range of cellular responses, including gene transcription, checkpoint activation, DNA repair, and others (Giglia-Mari et al., 2011; J. Y. Wang, 1998). Among these responses, DNA repair plays particularly important roles in maintaining genome stability (Sancar et al., 2004). This is because many types of DNA lesions are genotoxic by blocking DNA replication or gene transcription. Failure to repair them may lead to apoptosis (J. Y. J. Wang, 2001). Alternatively, if the cell does not die, the unrepaired damage can lead to mutations, which can cause several disease states, such as cancer or neurodegeneration (Chatterjee & Walker, 2017; Cooke et al., 2003; Giglia-Mari et al., 2011; Martin, 2008; Sancar et al., 2004).
Corresponding to the different types of DNA damage, cells are equipped with different repair pathways and are able to utilize the right repair mechanism for damage removal. There are several DNA repair pathways currently identified in the cell, including direct damage reversal, mismatch repair (MMR), base excision repair (BER), nucleotide excision repair (NER), single strand break repair (SSBR), and double strand break repair (DSBR) (Chatterjee & Walker, 2017; Martin, 2008). Direct damage reversal is exactly what the name implies: a direct reversal of the damage. Direct reversal repair enzymes include UV photolyase that repairs UV damage, O6-methylguanine-DNA-methyltransferase (MGMT) that repairs O6-alkylated bases, and the AlkB family that reverses N-alkylated base adducts (Yi & He, 2013). Direct reversal is highly specific for the damage type and only requires a single protein to conduct repair. MMR corrects mismatches between base pairs (i.e., non-A:T or G:C pairing) and insertions or deletions accumulated during replication and recombination. MMR has four major steps: mismatch recognition by MutS, recruitment of downstream MMR factors such as MutL, excision of DNA mismatch, and synthesis at the site using the remaining strand as a template (G.-M. Li, 2008). BER repairs small base damage in the nucleus and the mitochondria, such as oxidation, deamination, abasic sites, and alkylation lesions that do not cause distortions to the DNA helix. Within BER there are short-patch and long-patch pathways, requiring only a few key enzymes to carry out base excision, DNA backbone incision, end processing, repair synthesis, and ligation (Krokan & Bjørås, 2013). SSBR and DSBR are responsible for the repair of single-stranded and double-stranded breaks, respectively. In SSBR, breaks are recognized by the Poly (ADP-ribose) polymerase 1 (PARP1) protein and repair is conducted similar to the BER pathway (Ray Chaudhuri & Nussenzweig, 2017). DSBR has two major pathways to resolve double strand breaks, non-homologous end joining (NHEJ) and homologous recombination (HR) (Lieber, 2010; Scully et al., 2019).
NER is a versatile repair mechanism that removes a wide range of DNA adducts and plays a critical role for maintaining genome stability (Marteijn et al., 2014). Somewhat similar to BER, NER also conducts the ‘cut-and-patch’ type repair process; however, NER mainly removes helix-distorting lesions from the genome, such as UV photoproducts – cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs) formed by UV light, DNA adducts induced by benzopyrene in cigarettes, and crosslinks formed by cancer chemotherapeutics, such as cisplatin (Marteijn et al., 2014). These adducts can present different chemical modifications within the DNA; however, they are all bulky and helical distorting and can impede the progression of replication and transcription. As detailed below, NER performs ‘dual incision’ on both 5’ and 3’ sides of the damage to remove approximately 25-30 bases (Huang et al., 1992). The resulting gap on the damaged strand is subsequently filled by DNA polymerase and ligase (Marteijn et al., 2014; Prakash & Prakash, 2000; Schärer, 2013; Spivak, 2015).
Transcription factor IIH (TFIIH) is an essential protein complex for both transcription initiation and NER (Compe & Egly, 2012). In DNA repair, TFIIH mainly functions as a DNA helicase to unwind the two strands and promote assembly of the NER pre-incision complex. Additionally, TFIIH also plays a role in damage verification before the step of strand incision (Mu et al., 2018; Zurita & Cruz-Becerra, 2016). Here, we will discuss functions of TFIIH in NER and human genetic disorders associated with TFIIH deficiency.